[English] 日本語
Yorodumi
- PDB-3ic4: The crystal structure of the glutaredoxin(grx-1) from Archaeoglob... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ic4
TitleThe crystal structure of the glutaredoxin(grx-1) from Archaeoglobus fulgidus
ComponentsGlutaredoxin (Grx-1)
KeywordsOXIDOREDUCTASE / glutaredoxin(grx-1) / structural genomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


cell redox homeostasis / electron transfer activity
Similarity search - Function
: / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutaredoxin (Grx-1)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsZhang, R. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the glutaredoxin from Archaeoglobus fulgidus
Authors: Zhang, R. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJul 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutaredoxin (Grx-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7023
Polymers10,6531
Non-polymers492
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.951, 45.206, 45.461
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Glutaredoxin (Grx-1)


Mass: 10653.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF_1536, GI:2649025 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O28736
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes, 0.2M MgCl2, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 27, 2009 / Details: mirrows
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.7→99.4 Å / Num. all: 10152 / Num. obs: 10091 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 30.58
Reflection shellResolution: 1.7→1.744 Å / Redundancy: 7 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.13 / Num. unique all: 780 / % possible all: 97.44

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→32.06 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.463 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.118 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23865 510 4.8 %RANDOM
Rwork0.1949 ---
obs0.197 10091 99.4 %-
all-10152 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 4.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2--0.13 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms740 0 2 81 823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022754
X-RAY DIFFRACTIONr_bond_other_d0.0010.02540
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9781009
X-RAY DIFFRACTIONr_angle_other_deg0.8831316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.978591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.46723.82434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.815150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.423155
X-RAY DIFFRACTIONr_chiral_restr0.1050.2109
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02817
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02151
X-RAY DIFFRACTIONr_mcbond_it0.7891.5452
X-RAY DIFFRACTIONr_mcbond_other0.1731.5190
X-RAY DIFFRACTIONr_mcangle_it1.5732727
X-RAY DIFFRACTIONr_scbond_it2.9143302
X-RAY DIFFRACTIONr_scangle_it4.9834.5282
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 38 -
Rwork0.266 722 -
obs-760 97.44 %
Refinement TLS params.Method: refined / Origin x: 12.714 Å / Origin y: 29.541 Å / Origin z: 6.206 Å
111213212223313233
T0.1632 Å2-0.0033 Å20.0058 Å2-0.3562 Å2-0.0062 Å2--0.1931 Å2
L1.5068 °2-0.073 °20.0925 °2-1.3815 °2-0.6384 °2--1.1487 °2
S0.0589 Å °-0.0964 Å °-0.0855 Å °0.0928 Å °-0.0002 Å °0.0863 Å °0 Å °0.0233 Å °-0.0587 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-9 - 0
2X-RAY DIFFRACTION1A1 - 15
3X-RAY DIFFRACTION1A16 - 30
4X-RAY DIFFRACTION1A31 - 45
5X-RAY DIFFRACTION1A46 - 60
6X-RAY DIFFRACTION1A61 - 82

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more